Ernie Courtney played six years in the big leagues. After appearing on two teams in each of 1902 and 1903, he settled in with the Philadelphia Phillies in 1905-08, playing as a regular during the first three of those years. He led the 1905 National League in games played and was third in plate appearances and sacrifice hits.

Courtney was mainly a third baseman, but was also used liberally at the other infield positions (1B-SS-2B) as well as in left field.

He played for minor league teams based in California during 1898-1902. After stints in the majors during part of 1902 and in 1903, he played for Buffalo in 1904 before coming back to the majors in 1905-08. In 1909-10 he played for Providence and in 1911 he was with Memphis.